Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	t_alt_count	t_ref_count	validation_alt_allele	validation_method	validation_status	validation_tumor_sample	pox	qox	pox_cutoff	isArtifactMode	oxoGCut
LNX1	84708	broad.mit.edu	37	4	54362297	54362297	+	Missense_Mutation	SNP	C	C	T	rs139696663	byFrequency	TCGA-EB-A5VV-06A-11D-A32N-08	TCGA-EB-A5VV-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd1406e4-1221-43fe-b563-8a76b38d3f3b	8f0cfd03-2700-49af-87f5-8f4eb2f777c9	g.chr4:54362297C>T	ENST00000306888.2	-	5	1206	c.955G>A	c.(955-957)Ggt>Agt	p.G319S	LNX1_ENST00000263925.7_Missense_Mutation_p.G415S|FIP1L1_ENST00000507166.1_Intron	NM_032622.2	NP_116011.2	Q8TBB1	LNX1_HUMAN	ligand of numb-protein X 1, E3 ubiquitin protein ligase	415	PDZ 1.					cytoplasm	zinc ion binding			autonomic_ganglia(1)|breast(1)|central_nervous_system(3)|endometrium(3)|large_intestine(11)|lung(6)|ovary(3)|urinary_tract(4)	32	all_neural(26;0.153)		GBM - Glioblastoma multiforme(3;8.2e-46)|LUSC - Lung squamous cell carcinoma(32;0.0134)			TATGCCACACCGCCATCCAGC	0.502000													4	176					0	0	1	0	0
TAOK2	9344	broad.mit.edu	37	16	29989217	29989217	+	Missense_Mutation	SNP	G	G	A			TCGA-EB-A5VV-06A-11D-A32N-08	TCGA-EB-A5VV-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd1406e4-1221-43fe-b563-8a76b38d3f3b	8f0cfd03-2700-49af-87f5-8f4eb2f777c9	g.chr16:29989217G>A	ENST00000308893.4	+	2	1167	c.124G>A	c.(124-126)Gta>Ata	p.V42I	TAOK2_ENST00000279394.3_Missense_Mutation_p.V42I|TAOK2_ENST00000543033.1_Missense_Mutation_p.V42I	NM_001252043.1|NM_016151.3	NP_001238972.1|NP_057235.2	Q9UL54	TAOK2_HUMAN	TAO kinase 2	42	Protein kinase.				actin cytoskeleton organization|activation of MAPKK activity|apoptosis|cell migration|focal adhesion assembly|positive regulation of JNK cascade|protein targeting to membrane|regulation of cell growth|regulation of cell shape|response to stress	cytoplasmic vesicle membrane|cytoskeleton|dendrite|integral to membrane|nucleolus	ATP binding|protein serine/threonine kinase activity			breast(1)|endometrium(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(3)|skin(1)	22						CTTTGGAGCCGTATACTTTGT	0.532000													4	160					0	0	1	0	0
MT-ATP6	4508	broad.mit.edu	37	MT	8742	8742	+	Silent	SNP	A	A	G			TCGA-EB-A5VV-06A-11D-A32N-08	TCGA-EB-A5VV-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd1406e4-1221-43fe-b563-8a76b38d3f3b	8f0cfd03-2700-49af-87f5-8f4eb2f777c9	g.chrM:8742A>G	ENST00000361899.2	+	1	216	c.216A>G	c.(214-216)ctA>ctG	p.L72L						mitochondrially encoded ATP synthase 6											breast(2)|endometrium(7)|kidney(8)|prostate(1)	18						TCTCTTATACTAGTATCCTTA	0.408000													5	131					0	0	1	0	0
FAM102A	399665	broad.mit.edu	37	9	130712784	130712784	+	Missense_Mutation	SNP	G	G	A			TCGA-EB-A5VV-06A-11D-A32N-08	TCGA-EB-A5VV-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd1406e4-1221-43fe-b563-8a76b38d3f3b	8f0cfd03-2700-49af-87f5-8f4eb2f777c9	g.chr9:130712784G>A	ENST00000373095.1	-	4	707	c.332C>T	c.(331-333)gCg>gTg	p.A111V	FAM102A_ENST00000373084.4_5'UTR|FAM102A_ENST00000300434.3_5'UTR	NM_001035254.2	NP_001030331.1	Q5T9C2	F102A_HUMAN	family with sequence similarity 102, member A	111										breast(1)|cervix(1)|large_intestine(3)|lung(1)|ovary(4)	10						GCCCGAGCCCGCAAACTCGGC	0.632000													4	127					0	0	1	0	0
LINC01410	103352539	broad.mit.edu	37	9	66459909	66459909	+	RNA	SNP	T	T	C	rs146531631	by1000genomes	TCGA-EB-A5VV-06A-11D-A32N-08	TCGA-EB-A5VV-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd1406e4-1221-43fe-b563-8a76b38d3f3b	8f0cfd03-2700-49af-87f5-8f4eb2f777c9	g.chr9:66459909T>C	ENST00000424345.1	+	0	169																											cattaaaatcttgggcatgca	0.368000													3	20					0	0	1	0	0
IGDCC4	57722	broad.mit.edu	37	15	65678327	65678327	+	Missense_Mutation	SNP	C	C	A			TCGA-EB-A5VV-06A-11D-A32N-08	TCGA-EB-A5VV-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd1406e4-1221-43fe-b563-8a76b38d3f3b	8f0cfd03-2700-49af-87f5-8f4eb2f777c9	g.chr15:65678327C>A	ENST00000352385.2	-	18	3231	c.3022G>T	c.(3022-3024)Ggc>Tgc	p.G1008C		NM_020962.1	NP_066013.1	Q8TDY8	IGDC4_HUMAN	immunoglobulin superfamily, DCC subclass, member 4	1008						integral to membrane|plasma membrane		p.G1008C(1)		NS(1)|central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(24)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)	44						CTGGGGGGGCCAAGCCGAGCT	0.662000											OREG0023195	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	16					1.024e-07	1.06667e-07	1	1	0
LRRC7	57554	broad.mit.edu	37	1	70488952	70488952	+	Silent	SNP	G	G	A			TCGA-EB-A5VV-06A-11D-A32N-08	TCGA-EB-A5VV-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd1406e4-1221-43fe-b563-8a76b38d3f3b	8f0cfd03-2700-49af-87f5-8f4eb2f777c9	g.chr1:70488952G>A	ENST00000310961.5	+	18	2008	c.1590G>A	c.(1588-1590)caG>caA	p.Q530Q	LRRC7_ENST00000415775.2_Intron|RP11-181B18.1_ENST00000414132.1_RNA|LRRC7_ENST00000035383.5_Silent_p.Q525Q			Q96NW7	LRRC7_HUMAN	leucine rich repeat containing 7	525						centrosome|focal adhesion|nucleolus	protein binding			breast(11)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(3)|lung(81)|ovary(9)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	162						ATGACCCACAGCTGGCATGGG	0.547000													5	117					0	0	1	0	0
LINC01410	103352539	broad.mit.edu	37	9	66458345	66458345	+	RNA	SNP	G	G	A	rs2321645	by1000genomes	TCGA-EB-A5VV-06A-11D-A32N-08	TCGA-EB-A5VV-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd1406e4-1221-43fe-b563-8a76b38d3f3b	8f0cfd03-2700-49af-87f5-8f4eb2f777c9	g.chr9:66458345G>A	ENST00000424345.1	+	0	67																											CCCCGGGGCCGCGGGTCTCGG	0.751000													3	5					0	0	1	0	0
MN1	4330	broad.mit.edu	37	22	28194930	28194930	+	Silent	SNP	C	C	T			TCGA-EB-A5VV-06A-11D-A32N-08	TCGA-EB-A5VV-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd1406e4-1221-43fe-b563-8a76b38d3f3b	8f0cfd03-2700-49af-87f5-8f4eb2f777c9	g.chr22:28194930C>T	ENST00000302326.4	-	1	2556	c.1602G>A	c.(1600-1602)caG>caA	p.Q534Q		NM_002430.2	NP_002421.3	Q10571	MN1_HUMAN	meningioma (disrupted in balanced translocation) 1	534	Poly-Gln.						binding	p.Q550_R551insQ(1)		NS(1)|breast(2)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(6)|lung(15)|ovary(3)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	45						gctgctgctgctgttgctgct	0.647000			T	ETV6	"""AML, meningioma"""								3	13					0	0	1	0	0
HSD17B7P2	158160	broad.mit.edu	37	10	38654432	38654432	+	RNA	SNP	A	A	G	rs2257765		TCGA-EB-A5VV-06A-11D-A32N-08	TCGA-EB-A5VV-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd1406e4-1221-43fe-b563-8a76b38d3f3b	8f0cfd03-2700-49af-87f5-8f4eb2f777c9	g.chr10:38654432A>G	ENST00000494540.1	+	0	599					NR_003086.1																						TCATCTCGCAATGCAAGGAAA	0.453000													4	88					0	0	1	0	0
FAM57A	79850	broad.mit.edu	37	17	641146	641146	+	Silent	SNP	C	C	T			TCGA-EB-A5VV-06A-11D-A32N-08	TCGA-EB-A5VV-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd1406e4-1221-43fe-b563-8a76b38d3f3b	8f0cfd03-2700-49af-87f5-8f4eb2f777c9	g.chr17:641146C>T	ENST00000308278.8	+	3	503	c.267C>T	c.(265-267)taC>taT	p.Y89Y	FAM57A_ENST00000301324.8_Silent_p.Y89Y|FAM57A_ENST00000572018.1_Intron	NM_024792.1	NP_079068.1	Q8TBR7	FA57A_HUMAN	family with sequence similarity 57, member A	89	TLC.					integral to membrane|plasma membrane				cervix(1)|endometrium(2)|large_intestine(1)|lung(2)|prostate(2)|urinary_tract(2)	10				UCEC - Uterine corpus endometrioid carcinoma (25;0.0217)		ATGACTCGTACGCCATGTACC	0.502000													6	278					0	0	1	0	0
L1CAM	3897	broad.mit.edu	37	X	153130847	153130847	+	Missense_Mutation	SNP	G	G	A			TCGA-EB-A5VV-06A-11D-A32N-08	TCGA-EB-A5VV-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd1406e4-1221-43fe-b563-8a76b38d3f3b	8f0cfd03-2700-49af-87f5-8f4eb2f777c9	g.chrX:153130847G>A	ENST00000370060.1	-	21	2845	c.2656C>T	c.(2656-2658)Cgg>Tgg	p.R886W	L1CAM_ENST00000543994.1_Missense_Mutation_p.R888W|L1CAM_ENST00000538883.1_Missense_Mutation_p.R888W|L1CAM_ENST00000370057.3_Missense_Mutation_p.R886W|L1CAM_ENST00000370055.1_Missense_Mutation_p.R881W|L1CAM_ENST00000361981.3_Missense_Mutation_p.R881W|L1CAM_ENST00000361699.4_Missense_Mutation_p.R886W	NM_001278116.1	NP_001265045.1	P32004	L1CAM_HUMAN	L1 cell adhesion molecule	886	Fibronectin type-III 3.				axon guidance|blood coagulation|cell death|leukocyte migration	integral to membrane		p.R886W(1)		NS(1)|breast(4)|central_nervous_system(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|liver(1)|lung(31)|ovary(13)|pancreas(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	81	all_cancers(53;6.72e-15)|all_epithelial(53;3.19e-09)|all_lung(58;3.39e-06)|all_hematologic(71;4.25e-06)|Lung NSC(58;4.7e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					CTATAGGGCCGCAAGCCACTG	0.612000													4	228					0	0	1	0	0
TNKS	8658	broad.mit.edu	37	8	9609296	9609296	+	Missense_Mutation	SNP	G	G	A			TCGA-EB-A5VV-06A-11D-A32N-08	TCGA-EB-A5VV-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd1406e4-1221-43fe-b563-8a76b38d3f3b	8f0cfd03-2700-49af-87f5-8f4eb2f777c9	g.chr8:9609296G>A	ENST00000310430.6	+	19	3036	c.3010G>A	c.(3010-3012)Gta>Ata	p.V1004I	TNKS_ENST00000518281.1_Missense_Mutation_p.V767I	NM_003747.2	NP_003738.2	O95271	TNKS1_HUMAN	tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase	1004					mitotic spindle organization|mRNA transport|negative regulation of DNA binding|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of telomere maintenance via telomerase|protein auto-ADP-ribosylation|protein localization to chromosome, telomeric region|protein poly-ADP-ribosylation|protein polyubiquitination|protein transport|spindle assembly|transmembrane transport|Wnt receptor signaling pathway	chromosome, centromeric region|Golgi membrane|microsome|nuclear chromosome, telomeric region|nuclear membrane|nuclear pore|pericentriolar material	NAD+ ADP-ribosyltransferase activity|protein binding|zinc ion binding			NS(1)|endometrium(10)|kidney(6)|large_intestine(4)|lung(17)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)	49				COAD - Colon adenocarcinoma(149;0.0467)		AGAGTTGGCCGTAGGAGGAGC	0.542000													5	196					0	0	1	0	0
ESPNP	284729	broad.mit.edu	37	1	17021586	17021586	+	RNA	DEL	A	A	-			TCGA-EB-A5VV-06A-11D-A32N-08	TCGA-EB-A5VV-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd1406e4-1221-43fe-b563-8a76b38d3f3b	8f0cfd03-2700-49af-87f5-8f4eb2f777c9	g.chr1:17021586delA	ENST00000492551.1	-	0	1938					NR_026567.1																						gcccacgtataaggtggccgg	0.602													2	4	---	---	---	---					
LINC01057	101928079	broad.mit.edu	37	1	95170388	95170389	+	RNA	DEL	AG	AG	-			TCGA-EB-A5VV-06A-11D-A32N-08	TCGA-EB-A5VV-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd1406e4-1221-43fe-b563-8a76b38d3f3b	8f0cfd03-2700-49af-87f5-8f4eb2f777c9	g.chr1:95170388_95170389delAG	ENST00000452922.1	-	0	625																											agagagagaaagagagagagag	0.401													2	4	---	---	---	---					
LOC100506457	100506457	broad.mit.edu	37	2	12478631	12478631	+	RNA	DEL	T	T	-			TCGA-EB-A5VV-06A-11D-A32N-08	TCGA-EB-A5VV-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd1406e4-1221-43fe-b563-8a76b38d3f3b	8f0cfd03-2700-49af-87f5-8f4eb2f777c9	g.chr2:12478631delT	ENST00000412294.1	+	0	412																											TTGCTGATCATTTCCCAGGCC	0.458													2	4	---	---	---	---					
AC008074.4	0	broad.mit.edu	37	2	64725200	64725200	+	RNA	DEL	T	T	-			TCGA-EB-A5VV-06A-11D-A32N-08	TCGA-EB-A5VV-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd1406e4-1221-43fe-b563-8a76b38d3f3b	8f0cfd03-2700-49af-87f5-8f4eb2f777c9	g.chr2:64725200delT	ENST00000436433.1	+	0	186																											cggccttttcttttttttcag	0.507													2	4	---	---	---	---					
LOC101927958	101927958	broad.mit.edu	37	2	239140439	239140439	+	RNA	DEL	A	A	-			TCGA-EB-A5VV-06A-11D-A32N-08	TCGA-EB-A5VV-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd1406e4-1221-43fe-b563-8a76b38d3f3b	8f0cfd03-2700-49af-87f5-8f4eb2f777c9	g.chr2:239140439delA	ENST00000456601.1	+	0	115																											acaaacaaacaaaaaaacaCT	0.557													2	4	---	---	---	---					
ADAMTS9-AS2	100507098	broad.mit.edu	37	3	64830177	64830177	+	RNA	DEL	T	T	-			TCGA-EB-A5VV-06A-11D-A32N-08	TCGA-EB-A5VV-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd1406e4-1221-43fe-b563-8a76b38d3f3b	8f0cfd03-2700-49af-87f5-8f4eb2f777c9	g.chr3:64830177delT	ENST00000474768.1	+	0	573				ADAMTS9-AS2_ENST00000481312.1_RNA																							accagctaaatttttttttgt	0.512													2	4	---	---	---	---					
AC128709.2	0	broad.mit.edu	37	3	197186692	197186692	+	RNA	DEL	G	G	-	rs66973703		TCGA-EB-A5VV-06A-11D-A32N-08	TCGA-EB-A5VV-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd1406e4-1221-43fe-b563-8a76b38d3f3b	8f0cfd03-2700-49af-87f5-8f4eb2f777c9	g.chr3:197186692delG	ENST00000420213.1	+	0	138																											gcggtcgggaggggatgcggt	0.612													3	6	---	---	---	---					
RP11-802H3.2	0	broad.mit.edu	37	4	33436691	33436691	+	RNA	DEL	T	T	-			TCGA-EB-A5VV-06A-11D-A32N-08	TCGA-EB-A5VV-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd1406e4-1221-43fe-b563-8a76b38d3f3b	8f0cfd03-2700-49af-87f5-8f4eb2f777c9	g.chr4:33436691delT	ENST00000515263.1	+	0	55																											TTTGGTTCTGttttttttttt	0.378													3	3	---	---	---	---					
LOC728339	728339	broad.mit.edu	37	4	190797542	190797542	+	RNA	DEL	C	C	-			TCGA-EB-A5VV-06A-11D-A32N-08	TCGA-EB-A5VV-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd1406e4-1221-43fe-b563-8a76b38d3f3b	8f0cfd03-2700-49af-87f5-8f4eb2f777c9	g.chr4:190797542delC	ENST00000511785.1	-	0	231																											AGATTCATTTCTTTTCTACTA	0.294													2	4	---	---	---	---					
CTC-340D7.1	0	broad.mit.edu	37	5	68132571	68132571	+	RNA	DEL	T	T	-			TCGA-EB-A5VV-06A-11D-A32N-08	TCGA-EB-A5VV-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd1406e4-1221-43fe-b563-8a76b38d3f3b	8f0cfd03-2700-49af-87f5-8f4eb2f777c9	g.chr5:68132571delT	ENST00000503268.1	-	0	377																		p.0?(1)									ctcctgctccttctccttcac	0.468													2	4	---	---	---	---					
SLC27A6	28965	broad.mit.edu	37	5	128070139	128070139	+	RNA	DEL	A	A	-			TCGA-EB-A5VV-06A-11D-A32N-08	TCGA-EB-A5VV-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd1406e4-1221-43fe-b563-8a76b38d3f3b	8f0cfd03-2700-49af-87f5-8f4eb2f777c9	g.chr5:128070139delA	ENST00000514867.1	+	0	69																											cctccaacttaaaaaggactg	0.463													2	4	---	---	---	---					
LOC100996634	100996634	broad.mit.edu	37	6	109591512	109591512	+	Frame_Shift_Del	DEL	T	T	-			TCGA-EB-A5VV-06A-11D-A32N-08	TCGA-EB-A5VV-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd1406e4-1221-43fe-b563-8a76b38d3f3b	8f0cfd03-2700-49af-87f5-8f4eb2f777c9	g.chr6:109591512delT	ENST00000606661.1	+	10	1717	c.1717delT	c.(1717-1719)ttfs	p.F573fs	C6orf183_ENST00000453496.2_RNA	NM_001277339.1	NP_001264268.1																					ctactttctctttcctatctc	0.413													2	4	---	---	---	---					
RAET1E-AS1	100652739	broad.mit.edu	37	6	150203788	150203788	+	RNA	DEL	A	A	-	rs112489332		TCGA-EB-A5VV-06A-11D-A32N-08	TCGA-EB-A5VV-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd1406e4-1221-43fe-b563-8a76b38d3f3b	8f0cfd03-2700-49af-87f5-8f4eb2f777c9	g.chr6:150203788delA	ENST00000606915.1	+	0	889					NR_045126.1																						ccatatctataaaaaaaatct	0.507													2	4	---	---	---	---					
OSTCP1	202459	broad.mit.edu	37	6	159262511	159262512	+	RNA	INS	-	-	A			TCGA-EB-A5VV-06A-11D-A32N-08	TCGA-EB-A5VV-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd1406e4-1221-43fe-b563-8a76b38d3f3b	8f0cfd03-2700-49af-87f5-8f4eb2f777c9	g.chr6:159262511_159262512insA	ENST00000522287.1	-	0	831_832					NR_028496.1																						GTCAGCAGGGGAAAAAAAAATA	0.332													3	5	---	---	---	---					
CTD-2281E23.3	0	broad.mit.edu	37	8	1197216	1197217	+	RNA	INS	-	-	G	rs66848317	by1000genomes	TCGA-EB-A5VV-06A-11D-A32N-08	TCGA-EB-A5VV-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd1406e4-1221-43fe-b563-8a76b38d3f3b	8f0cfd03-2700-49af-87f5-8f4eb2f777c9	g.chr8:1197216_1197217insG	ENST00000517950.1	-	0	278																											GAGATCAGTGTGGAGTGATGGT	0.584													3	4	---	---	---	---					
KB-1043D8.6	0	broad.mit.edu	37	8	97248999	97249000	+	RNA	INS	-	-	T	rs72180922	by1000genomes	TCGA-EB-A5VV-06A-11D-A32N-08	TCGA-EB-A5VV-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd1406e4-1221-43fe-b563-8a76b38d3f3b	8f0cfd03-2700-49af-87f5-8f4eb2f777c9	g.chr8:97248999_97249000insT	ENST00000520575.1	+	0	135																											AAGGTTTTGGGttttttttgtt	0.441													5	2	---	---	---	---					
NAMA	100996569	broad.mit.edu	37	9	102121895	102121896	+	RNA	INS	-	-	C			TCGA-EB-A5VV-06A-11D-A32N-08	TCGA-EB-A5VV-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd1406e4-1221-43fe-b563-8a76b38d3f3b	8f0cfd03-2700-49af-87f5-8f4eb2f777c9	g.chr9:102121895_102121896insC	ENST00000604258.1	-	0	1815					NR_102270.1																						AAAGGACAGTGCCCCGGGAGCC	0.594													2	4	---	---	---	---					
CALML3-AS1	100132159	broad.mit.edu	37	10	5561481	5561482	+	RNA	INS	-	-	T	rs113181166		TCGA-EB-A5VV-06A-11D-A32N-08	TCGA-EB-A5VV-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd1406e4-1221-43fe-b563-8a76b38d3f3b	8f0cfd03-2700-49af-87f5-8f4eb2f777c9	g.chr10:5561481_5561482insT	ENST00000543008.1	-	0	1262				CALML3-AS1_ENST00000545372.1_RNA|CALML3-AS1_ENST00000542093.1_RNA																							atgaatgtgtgttttttttttg	0.426													2	4	---	---	---	---					
LINC00842	643650	broad.mit.edu	37	10	47109102	47109102	+	RNA	DEL	C	C	-	rs11318568		TCGA-EB-A5VV-06A-11D-A32N-08	TCGA-EB-A5VV-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd1406e4-1221-43fe-b563-8a76b38d3f3b	8f0cfd03-2700-49af-87f5-8f4eb2f777c9	g.chr10:47109102delC	ENST00000422732.2	-	0	435					NR_033957.1																						CTCCTGGGCACCTCACTCACC	0.577													5	4	---	---	---	---					
RP11-170M17.1	0	broad.mit.edu	37	10	65625829	65625830	+	RNA	INS	-	-	A	rs5785603	by1000genomes	TCGA-EB-A5VV-06A-11D-A32N-08	TCGA-EB-A5VV-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd1406e4-1221-43fe-b563-8a76b38d3f3b	8f0cfd03-2700-49af-87f5-8f4eb2f777c9	g.chr10:65625829_65625830insA	ENST00000444770.1	+	0	494																											CGGGAAGACTGAAAAAGATGTT	0.490											OREG0020209	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	2	4	---	---	---	---					
RP11-428C19.4	0	broad.mit.edu	37	11	19300239	19300239	+	RNA	DEL	G	G	-			TCGA-EB-A5VV-06A-11D-A32N-08	TCGA-EB-A5VV-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd1406e4-1221-43fe-b563-8a76b38d3f3b	8f0cfd03-2700-49af-87f5-8f4eb2f777c9	g.chr11:19300239delG	ENST00000527978.1	+	0	339																											ACAGGGATctggggctggggc	0.552													2	4	---	---	---	---					
RP11-631N16.2	0	broad.mit.edu	37	12	63000608	63000609	+	RNA	INS	-	-	C	rs11174559	by1000genomes	TCGA-EB-A5VV-06A-11D-A32N-08	TCGA-EB-A5VV-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd1406e4-1221-43fe-b563-8a76b38d3f3b	8f0cfd03-2700-49af-87f5-8f4eb2f777c9	g.chr12:63000608_63000609insC	ENST00000550290.1	+	0	84																											aaaaaaaaaaaaTCAATGTGAG	0.515													2	4	---	---	---	---					
RP11-897M7.1	0	broad.mit.edu	37	12	131962092	131962093	+	RNA	INS	-	-	ATA			TCGA-EB-A5VV-06A-11D-A32N-08	TCGA-EB-A5VV-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd1406e4-1221-43fe-b563-8a76b38d3f3b	8f0cfd03-2700-49af-87f5-8f4eb2f777c9	g.chr12:131962092_131962093insATA	ENST00000535133.1	-	0	195																											tggtaatggtggtggtgatggt	0.361													2	4	---	---	---	---					
RP11-266E6.3	0	broad.mit.edu	37	13	35222536	35222537	+	RNA	INS	-	-	ACTG	rs35142872	by1000genomes	TCGA-EB-A5VV-06A-11D-A32N-08	TCGA-EB-A5VV-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd1406e4-1221-43fe-b563-8a76b38d3f3b	8f0cfd03-2700-49af-87f5-8f4eb2f777c9	g.chr13:35222536_35222537insACTG	ENST00000606365.1	-	0	183																											tcaagttggtaactatgtctac	0.366													3	3	---	---	---	---					
RNF219-AS1	100874222	broad.mit.edu	37	13	78815355	78815356	+	RNA	INS	-	-	CA			TCGA-EB-A5VV-06A-11D-A32N-08	TCGA-EB-A5VV-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd1406e4-1221-43fe-b563-8a76b38d3f3b	8f0cfd03-2700-49af-87f5-8f4eb2f777c9	g.chr13:78815355_78815356insCA	ENST00000607862.1	+	0	230				RNF219-AS1_ENST00000560209.2_RNA|RNF219-AS1_ENST00000607860.1_RNA|RNF219-AS1_ENST00000430549.2_RNA|RNF219-AS1_ENST00000444769.3_RNA|RNF219-AS1_ENST00000607205.1_RNA|RNF219-AS1_ENST00000607220.1_RNA|RNF219-AS1_ENST00000606803.1_RNA|RNF219-AS1_ENST00000606376.1_RNA|RNF219-AS1_ENST00000606124.1_RNA|RNF219-AS1_ENST00000606187.1_RNA|RNF219-AS1_ENST00000605996.1_RNA|RNF219-AS1_ENST00000606429.1_RNA																							acatacacacgcacacacacac	0.342													2	4	---	---	---	---					
HERC2P3	283755	broad.mit.edu	37	15	20631337	20631337	+	RNA	DEL	C	C	-			TCGA-EB-A5VV-06A-11D-A32N-08	TCGA-EB-A5VV-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd1406e4-1221-43fe-b563-8a76b38d3f3b	8f0cfd03-2700-49af-87f5-8f4eb2f777c9	g.chr15:20631337delC	ENST00000428453.1	-	0	4041																				central_nervous_system(1)|endometrium(11)|kidney(2)|large_intestine(1)|lung(14)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	35						ttgtaagatacctgctgagag	0.348													2	4	---	---	---	---					
GOLGA6L2	283685	broad.mit.edu	37	15	23686010	23686011	+	In_Frame_Ins	INS	-	-	CTC			TCGA-EB-A5VV-06A-11D-A32N-08	TCGA-EB-A5VV-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd1406e4-1221-43fe-b563-8a76b38d3f3b	8f0cfd03-2700-49af-87f5-8f4eb2f777c9	g.chr15:23686010_23686011insCTC	ENST00000567107.1	-	8	1663_1664	c.1611_1612insGAG	c.(1609-1614)gaagat>gaGAGagat	p.537_538ED>ERD	GOLGA6L2_ENST00000345070.5_In_Frame_Ins_p.264_265ED>ERD|GOLGA6L2_ENST00000312015.5_In_Frame_Ins_p.537_538ED>ERD					golgin A6 family-like 2											breast(1)|endometrium(7)	8						tcccgcatcttctcctgccgcc	0.579													3	4	---	---	---	---					
RBFOX1	54715	broad.mit.edu	37	16	6069097	6069098	+	RNA	DEL	CA	CA	-			TCGA-EB-A5VV-06A-11D-A32N-08	TCGA-EB-A5VV-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd1406e4-1221-43fe-b563-8a76b38d3f3b	8f0cfd03-2700-49af-87f5-8f4eb2f777c9	g.chr16:6069097_6069098delCA	ENST00000569895.1	+	0	436																											gacacacacgcacacacacaca	0.530													2	4	---	---	---	---					
RN7SL245P	0	broad.mit.edu	37	16	22647903	22647904	+	RNA	INS	-	-	T			TCGA-EB-A5VV-06A-11D-A32N-08	TCGA-EB-A5VV-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd1406e4-1221-43fe-b563-8a76b38d3f3b	8f0cfd03-2700-49af-87f5-8f4eb2f777c9	g.chr16:22647903_22647904insT	ENST00000583924.1	-	0	161_162																											AAAATGTTGTGtttttttttct	0.470													2	4	---	---	---	---					
LINC01568	100506172	broad.mit.edu	37	16	73433858	73433858	+	RNA	DEL	A	A	-			TCGA-EB-A5VV-06A-11D-A32N-08	TCGA-EB-A5VV-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd1406e4-1221-43fe-b563-8a76b38d3f3b	8f0cfd03-2700-49af-87f5-8f4eb2f777c9	g.chr16:73433858delA	ENST00000554640.1	+	0	202																											CTGCATGCACAGTAACAGACG	0.458													2	4	---	---	---	---					
AC009120.6	0	broad.mit.edu	37	16	74353533	74353533	+	RNA	DEL	T	T	-			TCGA-EB-A5VV-06A-11D-A32N-08	TCGA-EB-A5VV-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd1406e4-1221-43fe-b563-8a76b38d3f3b	8f0cfd03-2700-49af-87f5-8f4eb2f777c9	g.chr16:74353533delT	ENST00000565313.1	-	0	47				AC009120.6_ENST00000561921.1_RNA																							tttcttcttcttttttttttt	0.493													2	4	---	---	---	---					
RPH3AL	9501	broad.mit.edu	37	17	203333	203333	+	RNA	DEL	A	A	-	rs11356209		TCGA-EB-A5VV-06A-11D-A32N-08	TCGA-EB-A5VV-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd1406e4-1221-43fe-b563-8a76b38d3f3b	8f0cfd03-2700-49af-87f5-8f4eb2f777c9	g.chr17:203333delA	ENST00000572499.1	+	0	225																											CCAAGGAGCCAGGGGTGTGGA	0.552													2	4	---	---	---	---					
FLJ36000	284124	broad.mit.edu	37	17	21911706	21911708	+	RNA	DEL	CTC	CTC	-			TCGA-EB-A5VV-06A-11D-A32N-08	TCGA-EB-A5VV-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd1406e4-1221-43fe-b563-8a76b38d3f3b	8f0cfd03-2700-49af-87f5-8f4eb2f777c9	g.chr17:21911706_21911708delCTC	ENST00000581223.2	+	0	2431_2433					NR_027084.1																						CACAGCTCTTCTCTGAGAACGAA	0.463													4	4	---	---	---	---					
RP11-640N20.8	0	broad.mit.edu	37	17	30419042	30419044	+	RNA	DEL	CCA	CCA	-			TCGA-EB-A5VV-06A-11D-A32N-08	TCGA-EB-A5VV-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd1406e4-1221-43fe-b563-8a76b38d3f3b	8f0cfd03-2700-49af-87f5-8f4eb2f777c9	g.chr17:30419042_30419044delCCA	ENST00000581225.1	-	0	72				RP11-640N20.6_ENST00000358484.4_RNA																							CCATCCCTCTCCACCACCACCAC	0.488													2	4	---	---	---	---					
LINC00669	647946	broad.mit.edu	37	18	36848204	36848205	+	RNA	INS	-	-	CA	rs34989487	by1000genomes	TCGA-EB-A5VV-06A-11D-A32N-08	TCGA-EB-A5VV-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd1406e4-1221-43fe-b563-8a76b38d3f3b	8f0cfd03-2700-49af-87f5-8f4eb2f777c9	g.chr18:36848204_36848205insCA	ENST00000591629.1	-	0	440					NR_024391.1																						ATACACACACGCACACACACAC	0.297													2	4	---	---	---	---					
MUC16	94025	broad.mit.edu	37	19	9038087	9038087	+	Frame_Shift_Del	DEL	G	G	-			TCGA-EB-A5VV-06A-11D-A32N-08	TCGA-EB-A5VV-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd1406e4-1221-43fe-b563-8a76b38d3f3b	8f0cfd03-2700-49af-87f5-8f4eb2f777c9	g.chr19:9038087delG	ENST00000397910.4	-	8	36392	c.36189delC	c.(36187-36189)ccfs	p.P12063fs		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	12065	Thr-rich.				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CTGTGGAGCTGGGGATGGAGG	0.493													2	4	---	---	---	---					
SCAF1	58506	broad.mit.edu	37	19	50155567	50155569	+	In_Frame_Del	DEL	AAG	AAG	-			TCGA-EB-A5VV-06A-11D-A32N-08	TCGA-EB-A5VV-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd1406e4-1221-43fe-b563-8a76b38d3f3b	8f0cfd03-2700-49af-87f5-8f4eb2f777c9	g.chr19:50155567_50155569delAAG	ENST00000360565.3	+	7	2045_2047	c.1921_1923delAAG	c.(1921-1923)del	p.K645del		NM_021228.2	NP_067051.2	Q9H7N4	SFR19_HUMAN	SR-related CTD-associated factor 1	645	Arg-rich.|Ser-rich.				mRNA processing|RNA splicing	nucleus	RNA binding			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	20		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.196)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00113)|GBM - Glioblastoma multiforme(134;0.0204)		TGGCGGCAGCAAGAAGAAGAAGA	0.744													2	4	---	---	---	---					
RP5-1121H13.4	0	broad.mit.edu	37	20	40658674	40658675	+	RNA	INS	-	-	A			TCGA-EB-A5VV-06A-11D-A32N-08	TCGA-EB-A5VV-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd1406e4-1221-43fe-b563-8a76b38d3f3b	8f0cfd03-2700-49af-87f5-8f4eb2f777c9	g.chr20:40658674_40658675insA	ENST00000431589.1	+	0	131																											ggagctcttccaacagaaactt	0.480													2	4	---	---	---	---					
BAGE2	85319	broad.mit.edu	37	21	11045983	11045983	+	RNA	DEL	A	A	-	rs57224481		TCGA-EB-A5VV-06A-11D-A32N-08	TCGA-EB-A5VV-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd1406e4-1221-43fe-b563-8a76b38d3f3b	8f0cfd03-2700-49af-87f5-8f4eb2f777c9	g.chr21:11045983delA	ENST00000470054.1	-	0	774									B melanoma antigen family, member 2															Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		TTCAAGTATCAAAACATTTAT	0.244													6	0	---	---	---	---					
BAGE2	85319	broad.mit.edu	37	21	11069158	11069158	+	RNA	DEL	T	T	-	rs57408407		TCGA-EB-A5VV-06A-11D-A32N-08	TCGA-EB-A5VV-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd1406e4-1221-43fe-b563-8a76b38d3f3b	8f0cfd03-2700-49af-87f5-8f4eb2f777c9	g.chr21:11069158delT	ENST00000470054.1	-	0	324									B melanoma antigen family, member 2															Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		gaataatatattaaaaaaaac	0.284													6	9	---	---	---	---					
LINC00112	54089	broad.mit.edu	37	21	43136672	43136672	+	RNA	DEL	C	C	-			TCGA-EB-A5VV-06A-11D-A32N-08	TCGA-EB-A5VV-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd1406e4-1221-43fe-b563-8a76b38d3f3b	8f0cfd03-2700-49af-87f5-8f4eb2f777c9	g.chr21:43136672delC	ENST00000432830.1	+	0	77					NR_024028.2																						CACAATCACTCCACCTCCCCA	0.552													2	4	---	---	---	---					
